When scanning my channels with my new antenna I have noticed that my TV indicates that it has found around 40 channels. When the TV is finished scanning I have around 13 channels that come in. Is there a setting that I am missing on my TV to view the remaining channels? or is the signal too weak on the remaining channels that they simply will out come in?

Check your "favorites" list to see if channels have been turned off or otherwise hidden.

Further, the "channel" tally usually is the sum of all sub-channels, not actual stations. Stations may carry multiple channels with 2-4 total channels per station being the most common implementation. 40 sub-channels across 13 stations would be a fairly average to just above average metro area.